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- PDB-6ak1: Crystal structure of DmoA from Hyphomicrobium sulfonivorans -

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Basic information

Entry
Database: PDB / ID: 6ak1
TitleCrystal structure of DmoA from Hyphomicrobium sulfonivorans
ComponentsDimethyl-sulfide monooxygenase
KeywordsOXIDOREDUCTASE / Dimethylsulfide monooxygenase / TIM barrel
Function / homology
Function and homology information


dissimilatory dimethyl sulfide monooxygenase / dimethyl sulfide monooxygenase activity
Similarity search - Function
Nitrilotriacetate monooxygenase component A/pristinamycin IIA synthase subunit A / Luciferase-like domain / Luciferase-like domain / Luciferase-like monooxygenase / Luciferase-like domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Dimethyl-sulfide monooxygenase
Similarity search - Component
Biological speciesHyphomicrobium sulfonivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.284 Å
AuthorsCao, H.Y. / Wang, P. / Peng, M. / Li, C.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31630012 China
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2018
Title: Crystal structure of the dimethylsulfide monooxygenase DmoA from Hyphomicrobium sulfonivorans.
Authors: Cao, H.Y. / Wang, P. / Peng, M. / Shao, X. / Chen, X.L. / Li, C.Y.
History
DepositionAug 28, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dimethyl-sulfide monooxygenase
B: Dimethyl-sulfide monooxygenase


Theoretical massNumber of molelcules
Total (without water)108,4972
Polymers108,4972
Non-polymers00
Water9,386521
1
A: Dimethyl-sulfide monooxygenase


Theoretical massNumber of molelcules
Total (without water)54,2491
Polymers54,2491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dimethyl-sulfide monooxygenase


Theoretical massNumber of molelcules
Total (without water)54,2491
Polymers54,2491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.190, 163.954, 116.674
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Dimethyl-sulfide monooxygenase / Dimethylsulfide monooxygenase large subunit


Mass: 54248.664 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hyphomicrobium sulfonivorans (bacteria)
Gene: dmoA / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: E9JFX9, dissimilatory dimethyl sulfide monooxygenase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 521 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 50.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Bis-Tris propane, PEG 3350, sodium iodide

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.28→50 Å / Num. obs: 47759 / % possible obs: 97.5 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 18.2
Reflection shellResolution: 2.28→2.38 Å / Rmerge(I) obs: 0.279 / Num. unique obs: 4320

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3B9O

3b9o


Resolution: 2.284→49.215 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.82
RfactorNum. reflection% reflection
Rfree0.2021 2343 4.91 %
Rwork0.1574 --
obs0.1596 47713 96.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.284→49.215 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7276 0 0 521 7797
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077436
X-RAY DIFFRACTIONf_angle_d0.82110078
X-RAY DIFFRACTIONf_dihedral_angle_d15.5594434
X-RAY DIFFRACTIONf_chiral_restr0.0491082
X-RAY DIFFRACTIONf_plane_restr0.0051328
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2843-2.33090.2281250.17512194X-RAY DIFFRACTION81
2.3309-2.38160.22791170.1762728X-RAY DIFFRACTION99
2.3816-2.4370.21221400.17482687X-RAY DIFFRACTION98
2.437-2.49790.21581430.17332679X-RAY DIFFRACTION99
2.4979-2.56540.24251430.17042734X-RAY DIFFRACTION99
2.5654-2.64090.23141390.1642710X-RAY DIFFRACTION100
2.6409-2.72620.24151280.16442707X-RAY DIFFRACTION99
2.7262-2.82360.21881630.16282657X-RAY DIFFRACTION98
2.8236-2.93660.20521240.16352709X-RAY DIFFRACTION98
2.9366-3.07030.22691570.16762702X-RAY DIFFRACTION98
3.0703-3.23210.21161330.16362681X-RAY DIFFRACTION97
3.2321-3.43460.19171420.15982721X-RAY DIFFRACTION98
3.4346-3.69970.17991370.14362703X-RAY DIFFRACTION98
3.6997-4.07180.17771380.13822667X-RAY DIFFRACTION96
4.0718-4.66060.18741240.13982662X-RAY DIFFRACTION95
4.6606-5.87040.18441390.1512716X-RAY DIFFRACTION96
5.8704-49.22640.19181510.16792713X-RAY DIFFRACTION93

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